In a biphasic (cyclohexane + water) tutorial (http://www.mdtutorials.com/gmx/biphasic/index.html) there is an inconsistency in the number of cyclohexane molecules.
First, it is stated that 1114 molecules were generated while the resulting chx_10ns.gro file has just 466 of them after NVT/NPT equilibration. What's going on?
Secondly, it is said in the beginning of the tutorial that "Details will not be given for simulation methodology, as there are numerous other tutorials that describe such workflows."
But there is a difference with the Lysozyme tutorial, for example, where there are charged particles and PME is used for treating electrostatics. Is it possible to learn how to make cyclohexane equilibration?
I'm trying to follow the steps from Lysozyme tutorial, but for the cyclohexane box the program suggests not to use PME. (a warning)
If I skip this warning (-maxwarn 1) then "segmentation fault" occurs when running "gmx mdrun" for NVT step. It could be accounted for by changing dt from 0.002 to 0.0002 for example, but that slows down the computation ten-fold.
Running NPT equilibration after the NVT step results in a npt.gro file having spatial dimensions of roughly 646^3 instead of initial 5^3. What's happend?